在芳香-芳香氨基酸相互作用中的堆叠和T形竞争
Riccardo Chelli1, Francesco Luigi Gervasio, Piero Procacci
1Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
Journal of the American Chemical Society
|May 23, 2002
概括
芳香氨基酸如氨酸和氨酸之间的相互作用主要堆叠在蛋白质中. 分子动力学模拟揭示了溶剂和距离对这些相互作用的影响,影响它们在蛋白质核或表面的发生.
科学领域:
- 计算化学是一种计算化学.
- 生物物理学的生物物理.
- 结构生物学是结构生物学.
背景情况:
- 芳香氨基酸,氨酸 (Phe) 和氨酸 (Tyr),对于蛋白质的结构和功能至关重要.
- 了解它们的相互作用,如堆叠和T形排列,是预测蛋白质折叠和稳定性的关键.
研究的目的:
- 为了研究相互作用的Phe-Phe,Phe-Tyr和Tyr-Tyr复合体的自由能量景观.
- 在各种溶剂和不同的几何约束下确定首选的相互作用模式 (堆叠与T形).
- 将模拟结果与实验蛋白质结构进行比较,以了解体内残留物相互作用模式.
主要方法:
- 分子动力学 (MD) 模拟来计算平均力 (PMF) 的潜力.
- 免费能量的表面计算,以分析堆叠和T形形状的形状.
- 对大型实验性蛋白质结构数据库 (2396个结构) 的分析.
- 沃罗诺伊多面体分析用于残留物的空间排列.
主要成果:
- 堆叠结构通常有利于Phe-Phe,Phe-Tyr和Tyr-Tyr复合物在溶剂中,除了Tyr-Tyr在四化碳中,T形结构也很重要.
- 短的C ((alpha) -C ((alpha) 距离有利于堆叠的安排,而长的距离有利于T形结构.
- 实验数据显示,Tyr-Tyr相互作用主要发生在蛋白质表面,而Phe-Phe和Phe-Tyr相互作用在疏水核中更为常见.
- 蛋白质分析证实,近端芳香残留物主要是堆叠的,远端的是T形的.
结论:
- 溶剂极性和残留物类型显著影响芳香氨基酸相互作用几何.
- 原子之间的距离是决定堆叠与T形相互作用的关键因素.
- 模拟结果与对蛋白质结构内芳香残留物定位的实验观测结果一致,区分核心和表面相互作用.
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